mergeBGMat               package:ScISI               R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _m_e_r_g_e_s _t_w_o _b_i_p_a_r_t_i_t_e _g_r_a_p_h (_B_G) _i_n_c_i_d_e_n_c_e
_m_a_t_r_i_c_e_s _i_n_t_o _o_n_e.

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes the union of the row names of mat1 and mat2
     for the row names of the aggregate matrix, and takes the union of
     the complexes of mat1 and mat2. The resulting matrix is also an
     incidence matrix so an entry of unity impiles protein p is a
     member of complex C.

_U_s_a_g_e:

     mergeBGMat(mat1, mat2, toBeRm)

_A_r_g_u_m_e_n_t_s:

    mat1: The first bipartite graph incidence matrix

    mat2: The second bipartite graph incidence matrix

  toBeRm: A character vector of complexes to be removed

_D_e_t_a_i_l_s:

     This function takes two bipartite graph matrices and merges them
     into one aggregate incidence matrix where informational redundancy
     is removed.

     The rows of the aggregate matrix is indexed by the union of the
     rownames of mat1 and mat2. It is important that the rownames of
     mat1 and the rownames of mat2 are from the same name set (e.g. for
     yeast, only the standard gene names should be used).

     The columns will be indexed by different protein complexes. If two
     protein complexes are identical, say C-i = K-j, then either C-i or
     K-j should be listed in toBeRm argument (given as an argument).
     When the matrices are merged, only one of the two will be kept.
     The vector toBeRm is generated by calling either
     'runCompareComplex' or 'findSubComp'.

_V_a_l_u_e:

     An aggregate bipartite graph incidence matrix.

_A_u_t_h_o_r(_s):

     Tony Chiang

_E_x_a_m_p_l_e_s:

     #go = getGOInfo()
     #mips = getMipsInfo()
     #goM = createGOMatrix(go)
     #mipsM = createMipsMatrix(mips)
     #cc = runCompareComplex(mipsM, goM, byWhich = "ROW")
     #merged = mergeBGMat(mipsM, goM, cc$toBeRm)

